From a44ac1ab59a27063911eb6a4e5987350162becad Mon Sep 17 00:00:00 2001
From: Foivos Gypas <fgypas@gmail.com>
Date: Thu, 17 May 2018 18:21:32 +0200
Subject: [PATCH] Small changes
---
snakemake/process_data/Snakefile | 24 ++++++++++--------------
snakemake/process_data/cluster.json | 2 +-
2 files changed, 11 insertions(+), 15 deletions(-)
diff --git a/snakemake/process_data/Snakefile b/snakemake/process_data/Snakefile
index c232957..c9a07d8 100644
--- a/snakemake/process_data/Snakefile
+++ b/snakemake/process_data/Snakefile
@@ -39,7 +39,7 @@ rule clip_reads:
flag = config["dir_created"],
reads = os.path.join(config["input_dir"], "{sample}" + config["input_reads_pattern"]),
output:
- reads = os.path.join(config["output_dir"], "{sample}/pro.clipped.fastq.gz"),
+ reads = os.path.join(config["output_dir"], "{sample}/pro.clipped.fastq"),
params:
v = "-v",
n = "-n",
@@ -59,7 +59,6 @@ rule clip_reads:
-l {params.l} \
{params.qual} \
-a {params.adapter} \
- {params.z} \
-i <(zcat {input.reads}) \
-o {output.reads}) &> {log}"
@@ -69,9 +68,9 @@ rule clip_reads:
rule trim_reads:
input:
- reads = os.path.join(config["output_dir"], "{sample}/pro.clipped.fastq.gz")
+ reads = os.path.join(config["output_dir"], "{sample}/pro.clipped.fastq")
output:
- reads = os.path.join(config["output_dir"], "{sample}/pro.trimmed.fastq.gz"),
+ reads = os.path.join(config["output_dir"], "{sample}/pro.trimmed.fastq"),
params:
v = "-v",
l = "20",
@@ -89,8 +88,7 @@ rule trim_reads:
-l {params.l} \
-t {params.t} \
{params.qual} \
- {params.z} \
- -i <(zcat {input.reads}) \
+ -i {input.reads} \
-o {output.reads}) &> {log}"
#################################################################################
@@ -99,15 +97,14 @@ rule trim_reads:
rule filter_reads:
input:
- reads = os.path.join(config["output_dir"], "{sample}/pro.trimmed.fastq.gz"),
+ reads = os.path.join(config["output_dir"], "{sample}/pro.trimmed.fastq"),
output:
- reads = os.path.join(config["output_dir"], "{sample}/pro.filtered.fastq.gz"),
+ reads = os.path.join(config["output_dir"], "{sample}/pro.filtered.fastq"),
params:
v = "-v",
q = "20",
p = "90",
qual = "-Q33",
- z = "-z",
cluster_log = os.path.join(config["cluster_log"], "filter_reads_{sample}.log")
log:
os.path.join(config["local_log"], "filter_reads_{sample}.log")
@@ -119,8 +116,7 @@ rule filter_reads:
-q {params.q} \
-p {params.p} \
{params.qual} \
- {params.z} \
- -i <(zcat {input.reads}) \
+ -i {input.reads} \
-o {output.reads}) &> {log}"
#################################################################################
@@ -129,7 +125,7 @@ rule filter_reads:
rule fastq_to_fasta:
input:
- reads = os.path.join(config["output_dir"], "{sample}/pro.filtered.fastq.gz"),
+ reads = os.path.join(config["output_dir"], "{sample}/pro.filtered.fastq"),
output:
reads = os.path.join(config["output_dir"], "{sample}/pro.filtered.fasta"),
params:
@@ -149,7 +145,7 @@ rule fastq_to_fasta:
{params.qual} \
{params.n} \
{params.r} \
- -i <(zcat {input.reads}) \
+ -i {input.reads} \
-o {output.reads}) &> {log}"
#################################################################################
@@ -190,7 +186,7 @@ rule map_to_other_genes:
rule map_to_transcripts:
input:
- reads = os.path.join(config["output_dir"], "{sample}/pro.filtered.fasta"),
+ reads = os.path.join(config["output_dir"], "{sample}/other_genes.unmapped.fasta"),
index = config["transcripts_index"],
sequence = config["transcripts_sequence"]
output:
diff --git a/snakemake/process_data/cluster.json b/snakemake/process_data/cluster.json
index 9af5fef..25fe29f 100644
--- a/snakemake/process_data/cluster.json
+++ b/snakemake/process_data/cluster.json
@@ -4,7 +4,7 @@
"queue":"6hours",
"time": "05:00:00",
"threads":"1",
-"mem":"4G"
+"mem":"8G"
},
"map_to_other_genes":
{
--
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